Multiple sequence alignment - TraesCS6B01G221700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G221700 chr6B 100.000 2162 0 0 1 2162 320210221 320212382 0 3993
1 TraesCS6B01G221700 chr2B 93.884 2191 100 11 1 2162 449211684 449209499 0 3273
2 TraesCS6B01G221700 chr2B 93.562 2190 105 10 1 2162 234533512 234531331 0 3230
3 TraesCS6B01G221700 chr3A 93.790 2190 104 9 1 2162 495094896 495092711 0 3262
4 TraesCS6B01G221700 chr3A 92.624 1654 85 11 1 1618 164858665 164860317 0 2344
5 TraesCS6B01G221700 chr7D 93.607 2190 111 9 1 2162 307047691 307049879 0 3241
6 TraesCS6B01G221700 chr7A 93.473 2191 111 11 1 2162 563514446 563512259 0 3225
7 TraesCS6B01G221700 chr7A 93.473 2191 111 11 1 2162 563581723 563579536 0 3225
8 TraesCS6B01G221700 chr7A 93.566 1803 84 9 388 2162 60222734 60220936 0 2658
9 TraesCS6B01G221700 chr1A 93.470 2190 114 5 1 2162 278531584 278533772 0 3225
10 TraesCS6B01G221700 chr1A 91.071 560 21 9 611 1141 554517573 554517014 0 730
11 TraesCS6B01G221700 chr6D 93.382 2191 113 10 1 2162 458920713 458918526 0 3214
12 TraesCS6B01G221700 chr3B 93.425 2190 108 11 1 2162 6003118 6000937 0 3214
13 TraesCS6B01G221700 chr3B 93.108 1654 78 6 1 1618 101916577 101914924 0 2390
14 TraesCS6B01G221700 chr3D 92.926 2191 125 9 1 2162 48691797 48693986 0 3160
15 TraesCS6B01G221700 chr3D 92.805 1654 82 7 1 1618 589271559 589273211 0 2361
16 TraesCS6B01G221700 chrUn 92.805 1654 81 7 1 1618 216513208 216514859 0 2361
17 TraesCS6B01G221700 chrUn 92.805 1654 81 7 1 1618 286270175 286268524 0 2361
18 TraesCS6B01G221700 chr5D 92.805 1654 82 7 1 1618 503223616 503221964 0 2361
19 TraesCS6B01G221700 chr5D 92.563 1654 87 10 1 1618 503273474 503275127 0 2340
20 TraesCS6B01G221700 chr5A 92.346 993 56 11 1 974 510134573 510135564 0 1395


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G221700 chr6B 320210221 320212382 2161 False 3993 3993 100.000 1 2162 1 chr6B.!!$F1 2161
1 TraesCS6B01G221700 chr2B 449209499 449211684 2185 True 3273 3273 93.884 1 2162 1 chr2B.!!$R2 2161
2 TraesCS6B01G221700 chr2B 234531331 234533512 2181 True 3230 3230 93.562 1 2162 1 chr2B.!!$R1 2161
3 TraesCS6B01G221700 chr3A 495092711 495094896 2185 True 3262 3262 93.790 1 2162 1 chr3A.!!$R1 2161
4 TraesCS6B01G221700 chr3A 164858665 164860317 1652 False 2344 2344 92.624 1 1618 1 chr3A.!!$F1 1617
5 TraesCS6B01G221700 chr7D 307047691 307049879 2188 False 3241 3241 93.607 1 2162 1 chr7D.!!$F1 2161
6 TraesCS6B01G221700 chr7A 563512259 563514446 2187 True 3225 3225 93.473 1 2162 1 chr7A.!!$R2 2161
7 TraesCS6B01G221700 chr7A 563579536 563581723 2187 True 3225 3225 93.473 1 2162 1 chr7A.!!$R3 2161
8 TraesCS6B01G221700 chr7A 60220936 60222734 1798 True 2658 2658 93.566 388 2162 1 chr7A.!!$R1 1774
9 TraesCS6B01G221700 chr1A 278531584 278533772 2188 False 3225 3225 93.470 1 2162 1 chr1A.!!$F1 2161
10 TraesCS6B01G221700 chr1A 554517014 554517573 559 True 730 730 91.071 611 1141 1 chr1A.!!$R1 530
11 TraesCS6B01G221700 chr6D 458918526 458920713 2187 True 3214 3214 93.382 1 2162 1 chr6D.!!$R1 2161
12 TraesCS6B01G221700 chr3B 6000937 6003118 2181 True 3214 3214 93.425 1 2162 1 chr3B.!!$R1 2161
13 TraesCS6B01G221700 chr3B 101914924 101916577 1653 True 2390 2390 93.108 1 1618 1 chr3B.!!$R2 1617
14 TraesCS6B01G221700 chr3D 48691797 48693986 2189 False 3160 3160 92.926 1 2162 1 chr3D.!!$F1 2161
15 TraesCS6B01G221700 chr3D 589271559 589273211 1652 False 2361 2361 92.805 1 1618 1 chr3D.!!$F2 1617
16 TraesCS6B01G221700 chrUn 216513208 216514859 1651 False 2361 2361 92.805 1 1618 1 chrUn.!!$F1 1617
17 TraesCS6B01G221700 chrUn 286268524 286270175 1651 True 2361 2361 92.805 1 1618 1 chrUn.!!$R1 1617
18 TraesCS6B01G221700 chr5D 503221964 503223616 1652 True 2361 2361 92.805 1 1618 1 chr5D.!!$R1 1617
19 TraesCS6B01G221700 chr5D 503273474 503275127 1653 False 2340 2340 92.563 1 1618 1 chr5D.!!$F1 1617
20 TraesCS6B01G221700 chr5A 510134573 510135564 991 False 1395 1395 92.346 1 974 1 chr5A.!!$F1 973

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
875 894 0.547712 AGGCCTTCCTCCACTAGCAA 60.548 55.0 0.0 0.0 38.72 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 1817 1.003355 GCTCCAACAGTGGCAGCTA 60.003 57.895 0.0 0.0 45.54 3.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.950544 TGTAGATGCTACATAGTGGGTTT 57.049 39.130 3.32 0.00 0.00 3.27
163 164 3.071457 TCTCAACCATTCTGACTTGCTCA 59.929 43.478 0.00 0.00 0.00 4.26
168 169 4.910195 ACCATTCTGACTTGCTCATACAA 58.090 39.130 0.00 0.00 0.00 2.41
186 187 2.686405 ACAAAACCAAGGTCGAAAGGAC 59.314 45.455 0.00 0.00 45.31 3.85
188 189 4.131596 CAAAACCAAGGTCGAAAGGACTA 58.868 43.478 0.00 0.00 45.35 2.59
193 194 4.820173 ACCAAGGTCGAAAGGACTAAAAAG 59.180 41.667 0.00 0.00 45.35 2.27
196 197 5.045012 AGGTCGAAAGGACTAAAAAGGTT 57.955 39.130 0.00 0.00 45.35 3.50
281 282 9.596677 TTCGAAATTGATTTCAAAAATGAATGC 57.403 25.926 14.73 0.00 44.83 3.56
354 355 8.522178 ACGAGTTCTAGTTTCTTTTATCACTG 57.478 34.615 0.00 0.00 0.00 3.66
362 363 4.908601 TTCTTTTATCACTGAGGAGCCA 57.091 40.909 0.00 0.00 0.00 4.75
411 412 6.294397 GGTTTTGCATGAGAGAAAGAAGTGAT 60.294 38.462 0.00 0.00 0.00 3.06
421 422 7.617329 TGAGAGAAAGAAGTGATGAATCCTCTA 59.383 37.037 0.00 0.00 0.00 2.43
452 453 0.613853 CTCCCCCACTCCAGTCGTTA 60.614 60.000 0.00 0.00 0.00 3.18
454 455 1.189524 CCCCCACTCCAGTCGTTACA 61.190 60.000 0.00 0.00 0.00 2.41
460 461 3.927142 CCACTCCAGTCGTTACATTTCTC 59.073 47.826 0.00 0.00 0.00 2.87
468 469 7.036220 CCAGTCGTTACATTTCTCTCTGTTAT 58.964 38.462 0.00 0.00 0.00 1.89
471 472 9.490379 AGTCGTTACATTTCTCTCTGTTATTTT 57.510 29.630 0.00 0.00 0.00 1.82
497 498 3.175724 CTGCTTCAGCTTCAGCCG 58.824 61.111 10.75 1.78 43.38 5.52
564 565 5.397334 GGCATCTTCTTCTGGAAATCCTAGT 60.397 44.000 0.44 0.00 36.82 2.57
568 569 9.487790 CATCTTCTTCTGGAAATCCTAGTTATC 57.512 37.037 0.44 0.00 36.82 1.75
748 766 5.772521 TCTAGGAACTTTTTCTTGCATTGC 58.227 37.500 0.46 0.46 41.75 3.56
791 809 7.707035 ACCAGAACTGATAACATTCGAGATTAC 59.293 37.037 3.19 0.00 0.00 1.89
793 811 7.644157 CAGAACTGATAACATTCGAGATTACGA 59.356 37.037 0.00 0.00 40.55 3.43
824 843 5.993441 ACAAATGAAAGATCCTTTTTGGCTG 59.007 36.000 6.30 0.00 35.26 4.85
875 894 0.547712 AGGCCTTCCTCCACTAGCAA 60.548 55.000 0.00 0.00 38.72 3.91
895 914 5.236695 AGCAAGTTTCTTCGGAAAACTCTAC 59.763 40.000 7.96 2.73 44.30 2.59
908 927 6.473758 GGAAAACTCTACCTATTCTGGTGTT 58.526 40.000 0.00 0.00 41.05 3.32
934 953 4.495911 GCAAGCAGGCCTATATTTCTTC 57.504 45.455 3.98 0.00 0.00 2.87
941 960 5.277538 GCAGGCCTATATTTCTTCGTTTCAG 60.278 44.000 3.98 0.00 0.00 3.02
958 978 5.393135 CGTTTCAGTAGACTCCTTATGAGCA 60.393 44.000 0.00 0.00 45.61 4.26
1164 1193 4.141597 GCTCAGGATACCCTCTTTTAGCTT 60.142 45.833 0.00 0.00 42.02 3.74
1192 1221 8.380742 AGGTCTATTTCTTAGTTCAAGATCCA 57.619 34.615 0.00 0.00 42.88 3.41
1341 1370 2.609459 CCAGACCGTGCACATTCTTATC 59.391 50.000 18.64 2.99 0.00 1.75
1352 1381 5.104402 TGCACATTCTTATCATGAGAAGGGA 60.104 40.000 25.64 16.74 38.76 4.20
1404 1433 4.186159 TGTTTACATAGAAAGCCCTACGC 58.814 43.478 0.00 0.00 37.98 4.42
1406 1435 1.200519 ACATAGAAAGCCCTACGCCA 58.799 50.000 0.00 0.00 38.78 5.69
1408 1437 2.224305 ACATAGAAAGCCCTACGCCATC 60.224 50.000 0.00 0.00 38.78 3.51
1461 1490 6.636454 AACCAGACCTCCTTTTGACATATA 57.364 37.500 0.00 0.00 0.00 0.86
1504 1533 1.952296 CATATGCACCTCTTTGGGCTC 59.048 52.381 0.00 0.00 41.11 4.70
1528 1557 8.752005 TCCTATTGAATCGAGAAATTGGATTT 57.248 30.769 13.06 0.00 34.78 2.17
1600 1637 9.214953 CAACAGATAAATCAAAACGAAGCTATC 57.785 33.333 0.00 0.00 0.00 2.08
1610 1647 3.724508 ACGAAGCTATCTGATGTCTGG 57.275 47.619 0.00 0.00 0.00 3.86
1641 1678 7.545615 GGCAAAAAGAAAAGAAAGAAGAGAACA 59.454 33.333 0.00 0.00 0.00 3.18
1659 1696 6.540551 AGAGAACAAAAGGAGAACAGAACTTC 59.459 38.462 0.00 0.00 0.00 3.01
1715 1752 7.530426 ACCTTGAATGCAATTTATAGATCCC 57.470 36.000 0.00 0.00 36.07 3.85
1717 1754 7.731688 ACCTTGAATGCAATTTATAGATCCCAT 59.268 33.333 0.00 0.00 36.07 4.00
1751 1788 5.404946 CCTCGGACTCGAAAAGTAATAACA 58.595 41.667 0.00 0.00 45.47 2.41
1780 1817 4.319177 GCTAATCCAATAGCAGATTCCGT 58.681 43.478 1.64 0.00 46.06 4.69
1859 1896 7.764695 AGAAACGGAAAATACCAAAAAGTTG 57.235 32.000 0.00 0.00 34.25 3.16
1946 1983 4.593634 AGGAGAATTCCCCGAATACCTAAG 59.406 45.833 0.65 0.00 45.24 2.18
2051 2088 2.909662 AGGCTTAGAAAGAAGTCCTGCT 59.090 45.455 0.00 0.00 34.03 4.24
2073 2110 1.133199 AGAGTCCAGGGAGAGCCTATG 60.133 57.143 0.00 0.00 0.00 2.23
2130 2171 3.430333 ACAACGCGTTTGATTTCCTTT 57.570 38.095 24.21 0.00 38.73 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.396478 CACTCGTAGTCTCTGAAGGATGAA 59.604 45.833 0.00 0.00 0.00 2.57
78 79 7.935664 TGACATGATCATCTTAGGGTGATCCC 61.936 46.154 21.62 11.03 46.40 3.85
100 101 2.325583 TCGTTCCCAATAGCCATGAC 57.674 50.000 0.00 0.00 0.00 3.06
149 150 5.769662 TGGTTTTGTATGAGCAAGTCAGAAT 59.230 36.000 0.00 0.00 39.07 2.40
163 164 4.517832 GTCCTTTCGACCTTGGTTTTGTAT 59.482 41.667 0.00 0.00 35.23 2.29
168 169 4.426736 TTAGTCCTTTCGACCTTGGTTT 57.573 40.909 0.00 0.00 43.08 3.27
186 187 7.860872 GTGGTTGTGAATGACTAACCTTTTTAG 59.139 37.037 0.00 0.00 42.32 1.85
188 189 6.379988 AGTGGTTGTGAATGACTAACCTTTTT 59.620 34.615 0.00 0.00 42.32 1.94
193 194 4.385825 TCAGTGGTTGTGAATGACTAACC 58.614 43.478 0.00 0.00 42.20 2.85
196 197 5.482163 TCATCAGTGGTTGTGAATGACTA 57.518 39.130 0.00 0.00 0.00 2.59
275 276 8.708742 GCGTATGTATAAGACTAAATGCATTCA 58.291 33.333 13.38 0.00 31.90 2.57
281 282 7.303261 TCCTCGCGTATGTATAAGACTAAATG 58.697 38.462 5.77 0.00 0.00 2.32
285 286 5.410746 CCTTCCTCGCGTATGTATAAGACTA 59.589 44.000 5.77 0.00 0.00 2.59
286 287 4.215827 CCTTCCTCGCGTATGTATAAGACT 59.784 45.833 5.77 0.00 0.00 3.24
338 339 5.221925 TGGCTCCTCAGTGATAAAAGAAACT 60.222 40.000 0.00 0.00 0.00 2.66
339 340 5.003804 TGGCTCCTCAGTGATAAAAGAAAC 58.996 41.667 0.00 0.00 0.00 2.78
354 355 0.105593 TTCATCTCGCATGGCTCCTC 59.894 55.000 0.00 0.00 0.00 3.71
362 363 2.871022 GCATGAGACTTTCATCTCGCAT 59.129 45.455 0.00 0.00 46.98 4.73
421 422 3.519913 GAGTGGGGGAGTAAGAGTTGAAT 59.480 47.826 0.00 0.00 0.00 2.57
425 426 1.151413 TGGAGTGGGGGAGTAAGAGTT 59.849 52.381 0.00 0.00 0.00 3.01
431 432 1.000019 CGACTGGAGTGGGGGAGTA 60.000 63.158 0.00 0.00 0.00 2.59
460 461 7.138692 AGCAGCTACTTTCAAAATAACAGAG 57.861 36.000 0.00 0.00 0.00 3.35
497 498 2.329379 AGGAATATCGAGAATTCGCGC 58.671 47.619 24.39 11.36 46.28 6.86
564 565 6.024563 TCCCCAAAATCATGCTAAGGATAA 57.975 37.500 0.00 0.00 0.00 1.75
568 569 4.897670 AGATTCCCCAAAATCATGCTAAGG 59.102 41.667 0.00 0.00 37.98 2.69
738 756 5.664294 AGACCAAATAATGCAATGCAAGA 57.336 34.783 13.45 3.06 43.62 3.02
791 809 7.559590 AGGATCTTTCATTTGTAATCCTTCG 57.440 36.000 0.00 0.00 39.95 3.79
801 819 5.993441 ACAGCCAAAAAGGATCTTTCATTTG 59.007 36.000 7.44 7.44 41.22 2.32
803 821 5.541484 AGACAGCCAAAAAGGATCTTTCATT 59.459 36.000 0.00 0.00 41.22 2.57
824 843 5.862678 AAGAGACATAGGGCTAAAGAGAC 57.137 43.478 0.00 0.00 0.00 3.36
875 894 5.548181 AGGTAGAGTTTTCCGAAGAAACT 57.452 39.130 9.49 9.49 41.69 2.66
895 914 3.003394 TGCCATCAACACCAGAATAGG 57.997 47.619 0.00 0.00 0.00 2.57
934 953 5.038033 GCTCATAAGGAGTCTACTGAAACG 58.962 45.833 0.00 0.00 45.88 3.60
941 960 7.496747 AGAAAGAATGCTCATAAGGAGTCTAC 58.503 38.462 0.00 0.00 45.88 2.59
1118 1147 5.732633 CAATTGCAAGAATGGGGTTCATTA 58.267 37.500 4.94 0.00 45.36 1.90
1341 1370 3.065655 GCTCGAATGATCCCTTCTCATG 58.934 50.000 0.00 0.00 33.69 3.07
1352 1381 5.738909 CCTATTTCCATAGGCTCGAATGAT 58.261 41.667 0.00 0.00 44.71 2.45
1396 1425 0.179045 AGAATGTGATGGCGTAGGGC 60.179 55.000 1.39 1.39 42.51 5.19
1440 1469 8.043710 GGATATATATGTCAAAAGGAGGTCTGG 58.956 40.741 11.14 0.00 0.00 3.86
1584 1621 6.257411 CAGACATCAGATAGCTTCGTTTTGAT 59.743 38.462 0.00 0.00 0.00 2.57
1585 1622 5.578336 CAGACATCAGATAGCTTCGTTTTGA 59.422 40.000 0.00 0.00 0.00 2.69
1590 1627 2.223923 GCCAGACATCAGATAGCTTCGT 60.224 50.000 0.00 0.00 0.00 3.85
1600 1637 0.035725 TTGCCTGAGCCAGACATCAG 60.036 55.000 4.00 0.00 42.14 2.90
1610 1647 5.351458 TCTTTCTTTTCTTTTTGCCTGAGC 58.649 37.500 0.00 0.00 40.48 4.26
1641 1678 7.255139 CCAAATACGAAGTTCTGTTCTCCTTTT 60.255 37.037 0.56 0.00 37.78 2.27
1659 1696 9.798994 ATAACTACAAGAGAGTTACCAAATACG 57.201 33.333 0.00 0.00 41.07 3.06
1713 1750 1.276421 CCGAGGGACTATTGCTATGGG 59.724 57.143 0.00 0.00 41.55 4.00
1780 1817 1.003355 GCTCCAACAGTGGCAGCTA 60.003 57.895 0.00 0.00 45.54 3.32
1804 1841 7.232910 TGATATGATGGGTCAATCATTTGCTA 58.767 34.615 6.19 0.00 43.28 3.49
1928 1965 7.246763 TCTCTATCTTAGGTATTCGGGGAATT 58.753 38.462 0.00 0.00 33.95 2.17
1994 2031 7.231115 TGAATTTCTCTGACATTCCATGTTTCA 59.769 33.333 0.00 0.00 45.03 2.69
2051 2088 1.011595 AGGCTCTCCCTGGACTCTAA 58.988 55.000 0.00 0.00 44.28 2.10
2130 2171 9.408648 GAAAGATGGAATTCCTTTGGTATAAGA 57.591 33.333 24.73 0.54 36.82 2.10


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.